liminal-orm 1.0.3__py3-none-any.whl → 1.0.4__py3-none-any.whl

liminal/base/base_dropdown.py

@@ -3,6 +3,16 @@ from typing import Any
 
 
 class BaseDropdown(ABC):
+    """_summary_
+
+    Parameters
+    ----------
+    __benchling_name__: str
+        The name of the dropdown in Benchling. There can be no duplicate dropdown names in Benchling.
+    __allowed_values__: list[str]
+        The list of values for the dropdown. Order matters and reflects the order of the dropdown in Benchling. Values must be unique.
+    """
+
     __benchling_name__: str
     __allowed_values__: list[str]
 

liminal/connection/benchling_service.py

@@ -27,9 +27,9 @@ class BenchlingService(Benchling):
         The connection object that contains the credentials for the Benchling tenant.
     use_api: bool
         Whether to connect to the Benchling SDK. Requires api_client_id and api_client_secret from the connection object.
-    use_db: bool
+    use_db: bool = False
         Whether to connect to the Benchling Postgres database. Requires warehouse_connection_string from the connection object.
-    use_internal_api: bool
+    use_internal_api: bool = False
         Whether to connect to the Benchling internal API. Requires internal_api_admin_email and internal_api_admin_password from the connection object.
     """
 

liminal/migrate/revision.py

@@ -165,7 +165,7 @@ class Revision(BaseModel):
         Path
             The path to the revision file that was written.
         """
-        created_date = datetime.now().strftime("%Y-%m-%d %H:%M:%S.%f")
+        created_date = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
         upgrade_operation_strings = [
             o.revision_file_string() for o in self.upgrade_operations
         ]

liminal/migrate/utils.py

@@ -15,8 +15,9 @@ def _check_env_file(env_file_path: Path) -> None:
 def read_local_env_file(
     env_file_path: Path, benchling_tenant: str
 ) -> tuple[str, BenchlingConnection]:
-    """Imports the env.py file from the current working directory and returns the CURRENT_REVISION_ID variable.
+    """Imports the env.py file from the current working directory and returns the CURRENT_REVISION_ID variable along with the BenchlingConnection object.
     The env.py file is expected to have the CURRENT_REVISION_ID variable set to the revision id you are currently on.
+    The BenchlingConnection object is expected to be defined and have connection information for the Benchling API client and internal API.
     """
     _check_env_file(env_file_path)
     module_path = Path.cwd() / env_file_path
@@ -26,22 +27,34 @@ def read_local_env_file(
     module = importlib.util.module_from_spec(spec)
     spec.loader.exec_module(module)
     for attr_name in dir(module):
-        attr = getattr(module, attr_name)
-        if isinstance(attr, BenchlingConnection) and (
-            benchling_tenant == attr.tenant_name
-            or benchling_tenant == attr.tenant_alias
-        ):
+        bc = getattr(module, attr_name)
+        if isinstance(bc, BenchlingConnection):
+            if not (
+                benchling_tenant == bc.tenant_name
+                or benchling_tenant == bc.tenant_alias
+            ):
+                raise Exception(
+                    f"tenant name {benchling_tenant} does not match tenant name {bc.tenant_name} or alias {bc.tenant_alias} in liminal/env.py."
+                )
+            if not bc.api_client_id or not bc.api_client_secret:
+                raise Exception(
+                    "api_client_id and api_client_secret must be provided in BenchlingConnection in liminal/env.py. This is necessary for the migration service."
+                )
+            if not bc.internal_api_admin_email or not bc.internal_api_admin_password:
+                raise Exception(
+                    "internal_api_admin_email and internal_api_admin_password must be provided in BenchlingConnection in liminal/env.py. This is necessary for the migration service."
+                )
             try:
                 current_revision_id: str = getattr(
-                    module, attr.current_revision_id_var_name
+                    module, bc.current_revision_id_var_name
                 )
-                return current_revision_id, attr
+                return current_revision_id, bc
             except Exception as e:
                 raise Exception(
-                    f"CURRENT_REVISION_ID variable not found in liminal/env.py. Given variable name: {attr.current_revision_id_var_name}"
+                    f"CURRENT_REVISION_ID variable not found in liminal/env.py. Given variable name: {bc.current_revision_id_var_name}"
                 ) from e
     raise Exception(
-        f"BenchlingConnection with tenant_name {benchling_tenant} not found in liminal/env.py. Please update the env.py file with the correctly defined BenchlingConnection."
+        "BenchlingConnection not found in liminal/env.py. Please update the env.py file with a correctly defined BenchlingConnection."
     )
 
 

liminal/orm/column.py

@@ -15,21 +15,21 @@ class Column(SqlColumn):
 
     Parameters
     ----------
-    name : str | None
+    name : str
         The external facing name of the field.
-    type : BenchlingFieldType | None
+    type : BenchlingFieldType
         The type of the field.
-    required : bool | None
+    required : bool
         Whether the field is required.
-    is_multi : bool | None
+    is_multi : bool = False
         Whether the field is a multi-value field.
-    parent_link : bool | None
+    parent_link : bool = False
         Whether the entity link field is a parent of the entity schema.
-    dropdown : str | None
-        The name of the dropdown for the field.
-    entity_link : str | None
+    dropdown : Type[BaseDropdown] | None = None
+        The dropdown for the field.
+    entity_link : str | None = None
         The warehouse name of the entity the field links to.
-    tooltip : str | None
+    tooltip : str | None = None
         The tooltip text for the field.
     """
 

{liminal_orm-1.0.3.dist-info → liminal_orm-1.0.4.dist-info}/METADATA

@@ -1,7 +1,8 @@
 Metadata-Version: 2.1
 Name: liminal-orm
-Version: 1.0.3
+Version: 1.0.4
 Summary: An ORM and toolkit that builds on top of Benchling's platform to keep your schemas and downstream code dependencies in sync.
+Home-page: https://github.com/dynotx/liminal-orm
 Author: DynoTx Open Source
 Author-email: opensource@dynotx.com
 Requires-Python: >=3.9,<4
@@ -19,26 +20,30 @@ Requires-Dist: rich (>=13.9.2,<14.0.0)
 Requires-Dist: sqlalchemy (<2)
 Requires-Dist: tenacity (>=8,<10)
 Requires-Dist: typer (>=0.12.5,<0.13.0)
+Project-URL: Bug Tracker, https://github.com/dynotx/liminal-orm/issues
+Project-URL: Documentation, https://dynotx.github.io/liminal-orm/
+Project-URL: Repository, https://github.com/dynotx/liminal-orm
 Description-Content-Type: text/markdown
 
 # [Liminal ORM](#liminal-orm)
 
-Liminal ORM<sup>1</sup> is a Python package that builds on top of [Benchling](https://www.benchling.com/)'s LIMS<sup>2</sup> platform to keep your Benchling schemas and downstream code dependencies in sync. Liminal provides an ORM framework using [SQLAlchemy](https://github.com/sqlalchemy/sqlalchemy) that allows you to define all your Benchling schemas in code. This creates a single source of truth that Benchling managers can use to keep multiple tenants in sync. This enables a code-first approach for managing Benchling tenants and accessing Benchling data. With the schemas defined in code, you can now take advantage of the additional capabilities that the Liminal toolkit provides. This includes:
+Liminal ORM<sup>1</sup> is an open-source Python package that builds on [Benchling's](https://www.benchling.com/) LIMS<sup>2</sup> platform and provides a simple framework to keep your upstream Benchling schemas and downstream dependencies in sync. Liminal provides an ORM framework using [SQLAlchemy](https://github.com/sqlalchemy/sqlalchemy) along with a schema migration service inspired by [Alembic](https://alembic.sqlalchemy.org/en/latest/). This allows you to define your Benchling schemas in code and create a *single source of truth* that synchronizes with your upstream Benchling tenant(s) and downstream dependencies. Through one line CLI commands, Liminal enables a code-first approach for managing Benchling tenants and accessing Benchling data. With the schemas defined in code, you can also take advantage of the additional capabilities that the Liminal toolkit provides. This includes:
 
-- The ability to run migrations to your Benchling tenant(s) through an easy to use CLI<sup>3</sup>.
+- The ability to run migrations to your Benchling tenant(s) through an easy to use CLI.
 - One source of truth defined in code for your Benchling schema model that your many Benchling tenants can stay in sync with.
 - Easy to implement validation rules to reflect business logic for all of your Benchling entities.
 - Strongly typed queries for all your Benchling entities.
 - CI/CD integration with GitHub Actions to ensure that your Benchling schemas and code are always in sync.
-- And more!
+- And more based on community contributions/feedback :)
 
 Benchling is an industry standard cloud platform for life sciences R&D. Liminal builds on top of Benchling's platform and assumes that you already have a Benchling tenant set up and have (or have access to) an admin user account. If not, learn more about getting started with Benchling [here](https://www.benchling.com/explore-benchling)!
 
-For a full and in-depth overview of Liminal, please refer to our [full documentation](https://dynotx.github.io/liminal-orm/). Below is a [quickstart guide](#getting-started) to get you Liminal set up in your project.
+If you are a Benchling user, try out Liminal by following the [quickstart guide](./getting-started/prerequisites.md)! Reach out in the [Discussions](https://github.com/dynotx/liminal-orm/discussions) forum with any questions or to simply introduce yourself! If there is something blocking you from using Liminal or you're having trouble setting Liminal up, please share in [Issues](https://github.com/dynotx/liminal-orm/issues) or reach out directly (contact information below). You can expect responses within 48 hours :)
 
-Reach out in the [Discussions](https://github.com/dynotx/liminal-orm/discussions) forum with any questions or to simply introduce yourself! If you run into any issues, during setup or usage, don't hesitate to post in [Issues](https://github.com/dynotx/liminal-orm/issues) or reach out directly at <opensource@dynotx.com>. You can expect responses within 48 hours :) 
+Nirmit Damania is the creator and current maintainer of Liminal (I post Liminal updates to [Discussions](https://github.com/dynotx/liminal-orm/discussions) and my [LinkedIn](https://www.linkedin.com/in/nirmit-damania/)). Most importantly, **you** have the ability to influence the future of Liminal! Any feedback, positive or negative, is highly encouraged and will be used to steer the direction of Liminal. Refer to the [Contributing guide](https://github.com/dynotx/liminal-orm/blob/main/CONTRIBUTING.md) to learn more about how you can contribute to Liminal.
 
 ⭐️ Leave a star on the repo to spread the word!
+If you or your organization use Liminal, please consider adding yourself or your organization to the [Users](https://github.com/dynotx/liminal-orm/blob/main/USERS.md) list.
 
 <img width="793" alt="liminal_simple_graph" src="https://github.com/user-attachments/assets/52e32cd0-3407-49f5-b100-5763bee3830c">
 
@@ -50,6 +55,7 @@ Reach out in the [Discussions](https://github.com/dynotx/liminal-orm/discussions
   - [Setup](#setup)
   - [Migration](#migration)
   - [Toolkit](#toolkit)
+- [Mission](#mission)
 - [Community](#community)
 - [Contributing](#contributing)
 - [License](#license)
@@ -141,18 +147,22 @@ With your schemas defined in code, you can now take advantage of the additional
 1. Entity validation: Easily create custom validation rules for your Benchling entities.
 
     ```python
-    from dyno.liminal.orm.base_model import BaseModel
-    from dyno.liminal.orm.mixins import CustomEntityMixin
-
-    class Pizza(BaseModel, CustomEntityMixin):
-        ...
-
-        @validator(BenchlingReportLevel.HIGH)
-        def cook_temp_time(self):
-            if self.cook_time is not None and self.cook_temp is None:
-                raise ValueError("Cook temp is required if cook time is set")
-            if self.cook_time is None and self.cook_temp is not None:
-                raise ValueError("Cook time is required if cook temp is set")
+    from liminal.validation import BenchlingValidator, BenchlingValidatorReport, BenchlingReportLevel
+    from liminal.orm.base_model import BaseModel
+
+    class CookTempValidator(BenchlingValidator):
+        """Validates that a field value is a valid enum value for a Benchling entity"""
+
+        def validate(self, entity: type[BaseModel]) -> BenchlingValidatorReport:
+            valid = True
+            message = None
+            if entity.cook_time is not None and entity.cook_temp is None:
+                valid = False
+                message = "Cook temp is required if cook time is set"
+            if entity.cook_time is None and entity.cook_temp is not None:
+                valid = False
+                message = "Cook time is required if cook temp is set"
+            return self.create_report(valid, BenchlingReportLevel.MED, entity, message)
     ```
 
 2. Strongly typed queries: Write type-safe queries using SQLAlchemy to access your Benchling entities.
@@ -167,6 +177,10 @@ With your schemas defined in code, you can now take advantage of the additional
 
 4. And more to come!
 
+## [Mission](#mission)
+
+The democratization of software in Biotech is crucial. By building a community around complex, yet common, problems and creating open-source solutions, we can work together to tackle these challenges together and enable faster innovation in the industry. By breaking down the silos between private platforms, we can enable a more dynamic and open ecosystem. This was the motivation for Liminal's creation. Liminal's goal is to create an open-source software product that enables a standard, code-first approach to configuration and change management for LIMS systems. We started with Benchling, but the goal is to make Liminal the go-to solution for any LIMS system.
+
 ## [Community](#community)
 
 We're excited to hear from you! Feel free to introduce yourself on the [Liminal GitHub Discussions page](https://github.com/dynotx/liminal-orm/discussions/categories/intros)
@@ -184,6 +198,11 @@ Please refer to [CONTRIBUTING.md](./CONTRIBUTING.md) to learn how to contribute
 
 Liminal ORM is distributed under the [Apache License, Version 2.0](./LICENSE.md).
 
+## [Direct Contact](#direct-contact)
+
+- Email: <opensource@dynotx.com>
+- LinkedIn: [Nirmit Damania](https://www.linkedin.com/in/nirmit-damania/)
+
 ## [Acknowledgements](#acknowledgements)
 
 This project could not have been started without the support of Dyno Therapeutics and the help of the following people.

{liminal_orm-1.0.3.dist-info → liminal_orm-1.0.4.dist-info}/RECORD

@@ -1,5 +1,5 @@
 liminal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-liminal/base/base_dropdown.py,sha256=cRJV-E1XDGO94pjXlRIwJag-tkJrNOKX6CTD_7Dk9r4,2167
+liminal/base/base_dropdown.py,sha256=Unk4l_5Y8rj_eSWYqzFi2BAFSQToQDWW2qdXwiCHTg8,2523
 liminal/base/base_operation.py,sha256=Yi0EOyLzXOFjiX4lGZW2mV_uo0lxfyRMs9-6HFVxf1w,3101
 liminal/base/base_validation_filters.py,sha256=2Q4QhqDSloZqc313p_fc8dnSw0uMhk_iMtsEtsC_5LQ,536
 liminal/base/compare_operation.py,sha256=hkpv4ewHhxy4dlTPKgJuzBjsAqO6Km7OrrKB44pRA_o,352
@@ -12,7 +12,7 @@ liminal/cli/live_test_dropdown_migration.py,sha256=i20JkY5xmLffHrB73WOl3Tjyb4V2R
 liminal/cli/live_test_entity_schema_migration.py,sha256=X03tEYYHYDXeXHWgLc9tcwksKVvr0b7nlYQndDS4MvA,5683
 liminal/connection/__init__.py,sha256=3z4pSANIOkc9mh1Xp763oYQuJZDEh4lauN901PU4vqI,166
 liminal/connection/benchling_connection.py,sha256=ZcKmaQE6T_yjAaSPF69e2PnhoZz5yZ_0TywjVykr0TM,2358
-liminal/connection/benchling_service.py,sha256=SEydyYUV3Zm55gAWs8tL2U9feLgbZITV_hH40aXIfBU,7397
+liminal/connection/benchling_service.py,sha256=DQDeRjgoUHeFisY5xZXJJ-Vb0xE8lu6hXj--j5kEvnU,7413
 liminal/dropdowns/api.py,sha256=n5oxi1EhkmpmPpNi1LOI4xcIQmk1C069XFaGP5XSBx8,6959
 liminal/dropdowns/compare.py,sha256=5cz8djtaStozUun_Cp8t_5PVjq-aovme2Qq5J8FXFg4,6829
 liminal/dropdowns/generate_files.py,sha256=IqnBs-IyLsIZE0NUkdB99zd5EAF-1f9CPBeblz-GzJE,2041
@@ -36,12 +36,12 @@ liminal/enums/benchling_sequence_type.py,sha256=TBI4C5c1XKE4ZXqsz1ApDUzy2wR-04u-
 liminal/external/__init__.py,sha256=5VrSpJ3wPedgoCrtMwvv2CM7u70KSwiTAt_1yU2Oje0,1052
 liminal/mappers.py,sha256=gevTAWU5nJe8hgUuOezhwFvnaVqVnURamafmq3w1fDU,8539
 liminal/migrate/components.py,sha256=ShkcYM3tfdfF01HbuPI_yrGpV8oxSLzJJ0tA1ZutQ3I,3328
-liminal/migrate/revision.py,sha256=0D8TbOO0aVcUpZoevqyDp_qkHNFaXy78aWOvVho9Pxw,7777
+liminal/migrate/revision.py,sha256=KppU0u-d0JsfPsXsmncxy9Q_XBJyf-o4e16wNZAJODM,7774
 liminal/migrate/revisions_timeline.py,sha256=06qf_7E1Hecucfczpm85rV3ATLDjpCf7y6TUfah5aLM,14450
-liminal/migrate/utils.py,sha256=0TOhlfCowqQ1WMp1O5VIGcULxbsfkvR5wdJJYcM7h7Q,2578
+liminal/migrate/utils.py,sha256=geVe2da2VB9wSaiv1-3GtTRM3l23fDDk3JQQCpUCZ48,3528
 liminal/orm/base.py,sha256=fFSpiNRYgK5UG7lbXdQGV8KgO8pwjMqt0pycM3rWJ2o,615
 liminal/orm/base_model.py,sha256=dLbhAFaD2hPEbEmAQTkMBRumkthGWdSd0YjHcbzE4hU,10925
-liminal/orm/column.py,sha256=robViEET2y0ugPxssOI4ZcDpVES6HSgeQ-0ZtyX4qSw,4504
+liminal/orm/column.py,sha256=dSYtqjpPgF2ECvw7CJ1AiMLGF8TdYT7IdaebIA0U_t8,4509
 liminal/orm/mixins.py,sha256=wm5DvI_6th94bfsgsbwzFSvTRbjEZfdT6R85J_NjvOc,4356
 liminal/orm/relationship.py,sha256=Zl4bMHbtDSPx1psGHYnojGGJpA8B8hwcPJdgjB1lmW0,2490
 liminal/orm/schema_properties.py,sha256=vZBOwS2SFtI6CjlYsaGno08TpXi47PC832mPmCJM3KI,2049
@@ -54,8 +54,8 @@ liminal/tests/test_dropdown_compare.py,sha256=yHB0ovQlBLRu8-qYkqIPd8VtYEOmOft_93
 liminal/tests/test_entity_schema_compare.py,sha256=FBYxqIB9oeFArWYKnbGV8I7NPzv2syziaPjEQg-wZ1o,15529
 liminal/utils.py,sha256=UT07vILwm9fu8DLgwIxMm1DxEPFIIsW-0mgBU8oNrNY,2566
 liminal/validation/__init__.py,sha256=SBd48xxBMJrBzI48G2RcK056EMlevt5YjmZMkfCWN1I,6924
-liminal_orm-1.0.3.dist-info/LICENSE.md,sha256=oVA877F_D1AV44dpjsv4f-4k690uNGApX1EtzOo3T8U,11353
-liminal_orm-1.0.3.dist-info/METADATA,sha256=kZKg7zRldnulEPHB9ryLiPzSs9EnRYil6QbJSBLJT48,11796
-liminal_orm-1.0.3.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
-liminal_orm-1.0.3.dist-info/entry_points.txt,sha256=atIrU63rrzH81dWC2sjUbFLlc5FWMmYRdMxXEWexIZA,47
-liminal_orm-1.0.3.dist-info/RECORD,,
+liminal_orm-1.0.4.dist-info/LICENSE.md,sha256=oVA877F_D1AV44dpjsv4f-4k690uNGApX1EtzOo3T8U,11353
+liminal_orm-1.0.4.dist-info/METADATA,sha256=qJ5daAJRXXiSRdnqu8hwiarlXrF8pkB85gcm1hORNBw,14118
+liminal_orm-1.0.4.dist-info/WHEEL,sha256=kLuE8m1WYU0Ig0_YEGrXyTtiJvKPpLpDEiChiNyei5Y,88
+liminal_orm-1.0.4.dist-info/entry_points.txt,sha256=atIrU63rrzH81dWC2sjUbFLlc5FWMmYRdMxXEWexIZA,47
+liminal_orm-1.0.4.dist-info/RECORD,,